Jonathan M. Irish, Ph.D.

Associate Professor

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Faculty Appointments
Associate Professor of Cell & Developmental Biology Associate Professor of Pathology, Microbiology and Immunology
Ph.D., Cancer Biology, Stanford University, Stanford, CaliforniaB.S., Chemistry, Biochemistry and Biology, University of Michigan, Ann Arbor, Michigan
Office Address
740B Preston Research Building
Irish Lab, Vanderbilt University
2220 Pierce Ave
Nashville, TN 37232-6840
Research Description
What makes our research different?
A defining feature of research in the Irish lab is the use of primary human tissue to reveal new cell types and dissect cell signaling mechanisms in healthy development and disease. Our group creates innovative technologies that measure the essential functions of millions of individual cells from patient biopsies. Our research is also distinguished by the creation and integrated use of bench and computational techniques. We aim to go beyond traditional model systems, such as immortalized cell lines or immune-deficient tumor models, and push the boundaries of single-cell biology to make fundamental discoveries about human cancer and immune cell signaling.

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Projects (updated for Fall 2020):  For trainees who join the lab, projects will be tailored to fit interests and available opportunities. Active research areas include: 1) signaling control of neural stem cell identity, 2) cancer and immune cell signaling interactions, 3) computational biology & machine learning for cell biology, and 3) identifying immune mechanisms of therapy response in human bone marrow, blood, germinal center, and tissue microenvironments. Rotations begin with training in our core technologies, such as phospho-specific flow cytometry, mass cytometry, and single cell data analysis.
Research Keywords
We study how signaling controls human cell identity. [ Keywords: Cancer, immunology, precision medicine, computational biology, machine learning, cell signaling, chemical biology, single cell tools. ]
Huse K, Bai B, Hilden VI, Bollum LK, Våtsveen TK, Munthe LA, Smeland EB, Irish JM, Wälchli S, Myklebust JH. Mechanism of CD79A and CD79B Support for IgM+ B Cell Fitness through B Cell Receptor Surface Expression. J Immunol [print-electronic]. 2022 Oct 10/10/2022; PMID: 36216512, PII: jimmunol.2200144, DOI: 10.4049/jimmunol.2200144, ISSN: 1550-6606.

Balsamo JA, Penton KE, Zhao Z, Hayes MJ, Lima SM, Irish JM, Bachmann BO. An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products. J Biol Chem [print-electronic]. 2022 Sep; 298(9): 102300. PMID: 35931117, PMCID: PMC9424577, PII: S0021-9258(22)00742-6, DOI: 10.1016/j.jbc.2022.102300, ISSN: 1083-351X.

Kaviany S, Bartkowiak T, Dulek DE, Khan YW, Hayes MJ, Schaefer SG, Ye X, Dahunsi DO, Connelly JA, Irish JM, Rathmell JC. Systems Immunology Analyses of STAT1 Gain-of-Function Immune Phenotypes Reveal Heterogeneous Response to IL-6 and Broad Immunometabolic Roles for STAT1. Immunohorizons. 2022 Jul 7/15/2022; 6(7): 447-64. PMID: 35840326, PMCID: PMC9623573, PII: immunohorizons.2200041, DOI: 10.4049/immunohorizons.2200041, ISSN: 2573-7732.

Kramer KJ, Wilfong EM, Voss K, Barone SM, Shiakolas AR, Raju N, Roe CE, Suryadevara N, Walker LM, Wall SC, Paulo A, Schaefer S, Dahunsi D, Westlake CS, Crowe JE, Carnahan RH, Rathmell JC, Bonami RH, Georgiev IS, Irish JM. Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine. Nat Commun. 2022 Jun 6/16/2022; 13(1): 3466. PMID: 35710908, PMCID: PMC9201272, PII: 10.1038/s41467-022-31142-5, DOI: 10.1038/s41467-022-31142-5, ISSN: 2041-1723.

Meghraoui-Kheddar A, Chousterman BG, Guillou N, Barone SM, Granjeaud S, Vallet H, Corneau A, Guessous K, de Roquetaillade C, Boissonnas A, Irish JM, Combadière C. Two New Neutrophil Subsets Define a Discriminating Sepsis Signature. Am J Respir Crit Care Med. 2022 Jan 1/1/2022; 205(1): 46-59. PMID: 34731593, DOI: 10.1164/rccm.202104-1027OC, ISSN: 1535-4970.

Wilfong EM, Bartkowiak T, Vowell KN, Westlake CS, Irish JM, Kendall PL, Crofford LJ, Bonami RH. High-Dimensional Analysis Reveals Distinct Endotypes in Patients With Idiopathic Inflammatory Myopathies. Front Immunol. 2022; 13: 756018. PMID: 35371068, PMCID: PMC8964392, DOI: 10.3389/fimmu.2022.756018, ISSN: 1664-3224.

Reisman BJ, Barone SM, Bachmann BO, Irish JM. DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Cytometry A [print-electronic]. 2021 Sep; 99(9): 946-53. PMID: 33960644, PMCID: PMC8410645, DOI: 10.1002/cyto.a.24363, ISSN: 1552-4930.

Ramsey HE, Stengel K, Pino JC, Johnston G, Childress M, Gorska AE, Arrate PM, Fuller L, Villaume M, Fischer MA, Ferrell PB, Roe CE, Zou J, Lubbock ALR, Stubbs M, Zinkel S, Irish JM, Lopez CF, Hiebert S, Savona MR. Selective Inhibition of JAK1 Primes STAT5-Driven Human Leukemia Cells for ATRA-Induced Differentiation. Target Oncol [print-electronic]. 2021 Sep; 16(5): 663-74. PMID: 34324169, PII: 10.1007/s11523-021-00830-5, DOI: 10.1007/s11523-021-00830-5, ISSN: 1776-260X.

Barone SM, Paul AG, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. Elife. 2021 Aug 8/5/2021; 10: PMID: 34350827, PMCID: PMC8370768, PII: 64653, DOI: 10.7554/eLife.64653, ISSN: 2050-084X.

Senosain MF, Zou Y, Novitskaya T, Vasiukov G, Balar AB, Rowe DJ, Doxie DB, Lehman JM, Eisenberg R, Maldonado F, Zijlstra A, Novitskiy SV, Irish JM, Massion PP. HLA-DR cancer cells expression correlates with T cell infiltration and is enriched in lung adenocarcinoma with indolent behavior. Sci Rep. 2021 Jul 7/13/2021; 11(1): 14424. PMID: 34257356, PMCID: PMC8277797, PII: 10.1038/s41598-021-93807-3, DOI: 10.1038/s41598-021-93807-3, ISSN: 2045-2322.

Yeh AC, Varelias A, Reddy A, Barone SM, Olver S, Chilson K, Onstad L, Ensbey KS, Henden AS, Samson L, Jaeger CA, Bi T, Dahlman K, Kim TK, Zhang P, Degli-Esposti MA, Newell EW, Jagasia M, Irish JM, Lee SJ, Hill GR. CMV exposure drives long-term CD57+ CD4 memory T cell inflation following allogeneic stem cell transplant. Blood [print-electronic]. 2021 Jun 6/3/2021; PMID: 34115118, PII: S0006-4971(21)01162-9, DOI: 10.1182/blood.2020009492, ISSN: 1528-0020.

Levine LS, Hiam-Galvez KJ, Marquez DM, Tenvooren I, Madden MZ, Contreras DC, Dahunsi DO, Irish JM, Oluwole OO, Rathmell JC, Spitzer MH. Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8+ T cells during the primary immune response. Immunity [print-electronic]. 2021 Apr 4/13/2021; 54(4): 829-844.e5. PMID: 33705706, PMCID: PMC8046726, PII: S1074-7613(21)00084-4, DOI: 10.1016/j.immuni.2021.02.018, ISSN: 1097-4180.

Healey DCC, Cephus JY, Barone SM, Chowdhury NU, Dahunsi DO, Madden MZ, Ye X, Yu X, Olszewski K, Young K, Gerriets VA, Siska PJ, Dworski R, Hemler J, Locasale JW, Poyurovsky MV, Peebles RS, Irish JM, Newcomb DC, Rathmell JC. Targeting In Vivo Metabolic Vulnerabilities of Th2 and Th17 Cells Reduces Airway Inflammation. J Immunol [print-electronic]. 2021 Mar 3/15/2021; 206(6): 1127-39. PMID: 33558372, PMCID: PMC7946768, PII: jimmunol.2001029, DOI: 10.4049/jimmunol.2001029, ISSN: 1550-6606.

Le Gallou S, Lhomme F, Irish JM, Mingam A, Pangault C, Monvoisin C, Ferrant J, Azzaoui I, Rossille D, Bouabdallah K, Damaj G, Cartron G, Godmer P, Le Gouill S, Casasnovas RO, Molina TJ, Houot R, Lamy T, Tarte K, Fest T, Roussel M. Nonclassical Monocytes Are Prone to Migrate Into Tumor in Diffuse Large B-Cell Lymphoma. Front Immunol. 2021; 12: 755623. PMID: 34975843, PMCID: PMC8716558, DOI: 10.3389/fimmu.2021.755623, ISSN: 1664-3224.

Beckermann KE, Hongo R, Ye X, Young K, Carbonell K, Healey DCC, Siska PJ, Barone S, Roe CE, Smith CC, Vincent BG, Mason FM, Irish JM, Rathmell WK, Rathmell JC. CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation. JCI Insight. 2020 Aug 8/20/2020; 5(16): PMID: 32814710, PMCID: PMC7455120, PII: 138729, DOI: 10.1172/jci.insight.138729, ISSN: 2379-3708.

Lim SP, Costantini B, Mian SA, Perez Abellan P, Gandhi S, Martinez Llordella M, Lozano JJ, Antunes Dos Reis R, Povoleri GAM, Mourikis TP, Abarrategi A, Ariza-McNaughton L, Heck S, Irish JM, Lombardi G, Marsh JCW, Bonnet D, Kordasti S, Mufti GJ. Treg sensitivity to FasL and relative IL-2 deprivation drive idiopathic aplastic anemia immune dysfunction. Blood. 2020 Aug 8/13/2020; 136(7): 885-97. PMID: 32294156, PII: 454391, DOI: 10.1182/blood.2019001347, ISSN: 1528-0020.

Barone SM, Paul AGA, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. BioRxiv. 2020 Aug 8/1/2020; PMID: 32766581, PMCID: PMC7402038, DOI: 10.1101/2020.07.31.190454.

Leelatian N, Sinnaeve J, Mistry AM, Barone SM, Brockman AA, Diggins KE, Greenplate AR, Weaver KD, Thompson RC, Chambless LB, Mobley BC, Ihrie RA, Irish JM. Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. Elife. 2020 Jun 6/23/2020; 9: PMID: 32573435, PMCID: PMC7340505, PII: 56879, DOI: 10.7554/eLife.56879, ISSN: 2050-084X.

Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. Curr Protoc Cytom. 2020 Mar; 93(1): e71. PMID: 32250555, DOI: 10.1002/cpcy.71, ISSN: 1934-9300.

Roussel M, Lhomme F, Roe CE, Bartkowiak T, Gravelle P, Laurent C, Fest T, Irish JM. Mass cytometry defines distinct immune profile in germinal center B-cell lymphomas. Cancer Immunol. Immunother [print-electronic]. 2020 Mar; 69(3): 407-20. PMID: 31919622, PII: 10.1007/s00262-019-02464-z, DOI: 10.1007/s00262-019-02464-z, ISSN: 1432-0851.

Ferrant J, Lhomme F, Le Gallou S, Irish JM, Roussel M. Circulating Myeloid Regulatory Cells: Promising Biomarkers in B-Cell Lymphomas. Front Immunol. 2020; 11: 623993. PMID: 33603754, PMCID: PMC7884747, DOI: 10.3389/fimmu.2020.623993, ISSN: 1664-3224.

Huse K, Wogsland CE, Polikowsky HG, Diggins KE, Smeland EB, Myklebust JH, Irish JM. Human Germinal Center B Cells Differ from Naïve and Memory B Cells in CD40 Expression and CD40L-Induced Signaling Response. Cytometry A [print-electronic]. 2019 Apr; 95(4): 442-9. PMID: 30838773, DOI: 10.1002/cyto.a.23737, ISSN: 1552-4930.

Rushing GV, Brockman AA, Bollig MK, Leelatian N, Mobley BC, Irish JM, Ess KC, Fu C, Ihrie RA. Location-dependent maintenance of intrinsic susceptibility to mTORC1-driven tumorigenesis. Life Sci Alliance [electronic-print]. 2019 Apr; 2(2): PMID: 30910807, PMCID: PMC6435042, PII: 2/2/e201800218, DOI: 10.26508/lsa.201800218, ISSN: 2575-1077.

Roussel M, Bartkowiak T, Irish JM. Picturing Polarized Myeloid Phagocytes and Regulatory Cells by Mass Cytometry. Methods Mol. Biol. 2019; 1989: 217-26. PMID: 31077108, DOI: 10.1007/978-1-4939-9454-0_14, ISSN: 1940-6029.

Mistry AM, Greenplate AR, Ihrie RA, Irish JM. Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors. FEBS J [print-electronic]. 2018 Dec 12/13/2018; PMID: 30549207, DOI: 10.1111/febs.14730, ISSN: 1742-4658.

Greenplate AR, McClanahan DD, Oberholtzer BK, Doxie DB, Roe CE, Diggins KE, Leelatian N, Rasmussen ML, Kelley MC, Gama V, Siska PJ, Rathmell JC, Ferrell PB, Johnson DB, Irish JM. Computational immune monitoring reveals abnormal double negative T cells present across human tumor types. Cancer Immunol Res [print-electronic]. 2018 Nov 11/9/2018; PMID: 30413431, PII: 2326-6066.CIR-17-0692, DOI: 10.1158/2326-6066.CIR-17-0692, ISSN: 2326-6074.

Gandelman JS, Byrne MT, Mistry AM, Polikowsky HG, Diggins KE, Chen H, Lee SJ, Arora M, Cutler C, Flowers M, Pidala J, Irish JM, Jagasia MH. Machine learning reveals chronic graft-versus-host disease phenotypes and stratifies survival after stem cell transplant for hematologic malignancies. Haematologica [print-electronic]. 2018 Sep 9/20/2018; PMID: 30237265, PII: haematol.2018.193441, DOI: 10.3324/haematol.2018.193441, ISSN: 1592-8721.

Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM. BRAF and MEK inhibitor therapy eliminates nestin expressing melanoma cells in human tumors. Pigment Cell Melanoma Res [print-electronic]. 2018 May 5/19/2018; PMID: 29778085, DOI: 10.1111/pcmr.12712, ISSN: 1755-148X.

Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM). Curr Protoc Cytom. 2018 Jan 1/18/2018; 83: 10.21.1-10.21.28. PMID: 29345329, PMCID: PMC5774653, DOI: 10.1002/cpcy.34, ISSN: 1934-9300.

Earl DC, Ferrell PB, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO. Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics. Nat Commun. 2018 Jan 1/2/2018; 9(1): 39. PMID: 29295987, PII: 10.1038/s41467-017-02470-8, DOI: 10.1038/s41467-017-02470-8, ISSN: 2041-1723.

Greenplate A, Wang K, Tripathi RM, Palma N, Ali SM, Stephens PJ, Miller VA, Shyr Y, Guo Y, Reddy NM, Kozhaya L, Unutmaz D, Chen X, Irish JM, Davé UP. Genomic Profiling of T-Cell Neoplasms Reveals Frequent JAK1 and JAK3 Mutations With Clonal Evasion From Targeted Therapies. JCO Precis Oncol [print-electronic]. 2018; 2018: PMID: 30079384, PMCID: PMC6072266, DOI: 10.1200/PO.17.00019, ISSN: 2473-4284.

Josefsson SE, Huse K, Kolstad A, Beiske K, Pende D, Steen CB, Inderberg EM, Lingjærde OC, Østenstad B, Smeland EB, Levy R, Irish JM, Myklebust JH. T cells expressing checkpoint receptor TIGIT are enriched in follicular lymphoma tumors and characterized by reversible suppression of T-cell receptor signaling. Clin. Cancer Res [print-electronic]. 2017 Dec 12/7/2017; PMID: 29217528, PII: 1078-0432.CCR-17-2337, DOI: 10.1158/1078-0432.CCR-17-2337, ISSN: 1078-0432.

Roussel M, Irish JM, Menard C, Lhomme F, Tarte K, Fest T. Regulatory myeloid cells: an underexplored continent in B-cell lymphomas. Cancer Immunol. Immunother [print-electronic]. 2017 Jul 7/8/2017; PMID: 28689360, PII: 10.1007/s00262-017-2036-5, DOI: 10.1007/s00262-017-2036-5, ISSN: 1432-0851.

Siska PJ, Beckermann KE, Mason FM, Andrejeva G, Greenplate AR, Sendor AB, Chiang YJ, Corona AL, Gemta LF, Vincent BG, Wang RC, Kim B, Hong J, Chen CL, Bullock TN, Irish JM, Rathmell WK, Rathmell JC. Mitochondrial dysregulation and glycolytic insufficiency functionally impair CD8 T cells infiltrating human renal cell carcinoma. JCI Insight [print-electronic]. 2017 Jun 6/15/2017; 2(12): PMID: 28614802, PMCID: PMC5470888, PII: 93411, DOI: 10.1172/jci.insight.93411, ISSN: 2379-3708.

Roussel M, Ferrell PB, Greenplate AR, Lhomme F, Le Gallou S, Diggins KE, Johnson DB, Irish JM. Mass cytometry deep phenotyping of human mononuclear phagocytes and myeloid-derived suppressor cells from human blood and bone marrow. J. Leukoc. Biol [print-electronic]. 2017 Apr 4/11/2017; PMID: 28400539, PII: jlb.5MA1116-457R, DOI: 10.1189/jlb.5MA1116-457R, ISSN: 1938-3673.

Leelatian N, Doxie DB, Greenplate AR, Sinnaeve J, Ihrie RA, Irish JM. Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis. Curr Protoc Mol Biol. 2017 Apr 4/3/2017; 118: 25C.1.1-25C.1.23. PMID: 28369679, DOI: 10.1002/cpmb.37, ISSN: 1934-3647.

Diggins KE, Greenplate AR, Leelatian N, Wogsland CE, Irish JM. Characterizing cell subsets using marker enrichment modeling. Nat. Methods [print-electronic]. 2017 Mar; 14(3): 275-8. PMID: 28135256, PMCID: PMC5330853, PII: nmeth.4149, DOI: 10.1038/nmeth.4149, ISSN: 1548-7105.

Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V. Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. Cancer Res [print-electronic]. 2017 Mar 3/1/2017; 77(5): 1063-74. PMID: 27932399, PII: 0008-5472.CAN-16-1467, DOI: 10.1158/0008-5472.CAN-16-1467, ISSN: 1538-7445.

Myklebust JH, Brody J, Kohrt HE, Kolstad A, Czerwinski DK, Wälchli S, Green MR, Trøen G, Liestøl K, Beiske K, Houot R, Delabie J, Alizadeh AA, Irish JM, Levy R. Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling. Blood [print-electronic]. 2017 Feb 2/9/2017; 129(6): 759-70. PMID: 28011673, PMCID: PMC5301824, PII: blood-2016-05-718494, DOI: 10.1182/blood-2016-05-718494, ISSN: 1528-0020.

Wogsland CE, Greenplate AR, Kolstad A, Myklebust JH, Irish JM, Huse K. Mass Cytometry of Follicular Lymphoma Tumors Reveals Intrinsic Heterogeneity in Proteins Including HLA-DR and a Deficit in Nonmalignant Plasmablast and Germinal Center B-Cell Populations. Cytometry B Clin Cytom. 2017 Jan; 92(1): 79-87. PMID: 27933753, DOI: 10.1002/cyto.b.21498, ISSN: 1552-4957.

Leelatian N, Doxie DB, Greenplate AR, Mobley BC, Lehman JM, Sinnaeve J, Kauffmann RM, Werkhaven JA, Mistry AM, Weaver KD, Thompson RC, Massion PP, Hooks MA, Kelley MC, Chambless LB, Ihrie RA, Irish JM. Single cell analysis of human tissues and solid tumors with mass cytometry. Cytometry B Clin Cytom [print-electronic]. 2017 Jan; 92(1): 68-78. PMID: 27598832, DOI: 10.1002/cyto.b.21481, ISSN: 1552-4957.

Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal. 2016 Oct 10/11/2016; 9(449): rs11. PMID: 27729552, PMCID: PMC5111815, PII: 9/449/rs11, DOI: 10.1126/scisignal.aah4413, ISSN: 1937-9145.

Kordasti S, Costantini B, Seidl T, Perez Abellan P, Martinez Llordella M, McLornan D, Diggins KE, Kulasekararaj A, Benfatto C, Feng X, Smith A, Mian SA, Melchiotti R, de Rinaldis E, Ellis R, Petrov N, Povoleri GA, Chung SS, Thomas NS, Farzaneh F, Irish JM, Heck S, Young NS, Marsh JC, Mufti GJ. Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment. Blood [print-electronic]. 2016 Sep 9/1/2016; 128(9): 1193-205. PMID: 27281795, PMCID: PMC5009512, PII: blood-2016-03-703702, DOI: 10.1182/blood-2016-03-703702, ISSN: 1528-0020.

Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol. Syst. Biol. 2016 Aug 8/29/2016; 12(8): 881. PMID: 27574014, PMCID: PMC5119492, ISSN: 1744-4292.

Greenplate AR, Johnson DB, Ferrell PB, Irish JM. Systems immune monitoring in cancer therapy. Eur. J. Cancer [print-electronic]. 2016 Jul; 61: 77-84. PMID: 27155446, PMCID: PMC4885747, PII: S0959-8049(16)32047-0, DOI: 10.1016/j.ejca.2016.03.085, ISSN: 1879-0852.

Greenplate AR, Johnson DB, Roussel M, Savona MR, Sosman JA, Puzanov I, Ferrell PB, Irish JM. Myelodysplastic Syndrome Revealed by Systems Immunology in a Melanoma Patient Undergoing Anti-PD-1 Therapy. Cancer Immunol Res [print-electronic]. 2016 Mar 3/10/2016; PMID: 26966176, PII: 2326-6066.CIR-15-0213, DOI: 10.1158/2326-6066.CIR-15-0213, ISSN: 2326-6074.

Chong KM, Leelatian N, Deguire SM, Brockman AA, Earl D, Ihrie RA, Irish JM, Bachmann BO, Sulikowski GA. The use of fluorescently-tagged apoptolidins in cellular uptake and response studies. J. Antibiot [print-electronic]. 2016 Mar 3/9/2016; PMID: 26956792, PII: ja201622, DOI: 10.1038/ja.2016.22, ISSN: 0021-8820.

Johnson DB, Estrada MV, Salgado R, Sanchez V, Doxie DB, Opalenik SR, Vilgelm AE, Feld E, Johnson AS, Greenplate AR, Sanders ME, Lovly CM, Frederick DT, Kelley MC, Richmond A, Irish JM, Shyr Y, Sullivan RJ, Puzanov I, Sosman JA, Balko JM. Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy. Nat Commun. 2016; 7: 10582. PMID: 26822383, PMCID: PMC4740184, PII: ncomms10582, DOI: 10.1038/ncomms10582, ISSN: 2041-1723.

Ferrell PB, Diggins KE, Polikowsky HG, Mohan SR, Seegmiller AC, Irish JM. High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy. PLoS ONE. 2016; 11(4): e0153207. PMID: 27074138, PMCID: PMC4830605, PII: PONE-D-15-20447, DOI: 10.1371/journal.pone.0153207, ISSN: 1932-6203.

Shah AT, Diggins KE, Walsh AJ, Irish JM, Skala MC. In Vivo Autofluorescence Imaging of Tumor Heterogeneity in Response to Treatment. Neoplasia. 2015 Dec; 17(12): 862-70. PMID: 26696368, PII: S1476-5586(15)00143-8, DOI: 10.1016/j.neo.2015.11.006, ISSN: 1476-5586.

Nicholas KJ, Greenplate AR, Flaherty DK, Matlock BK, Juan JS, Smith RM, Irish JM, Kalams SA. Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry. Cytometry A [print-electronic]. 2015 Nov 11/24/2015; PMID: 26599989, DOI: 10.1002/cyto.a.22799, ISSN: 1552-4930.

Polikowsky HG, Wogsland CE, Diggins KE, Huse K, Irish JM. Cutting Edge: Redox Signaling Hypersensitivity Distinguishes Human Germinal Center B Cells. J. Immunol [print-electronic]. 2015 Aug 8/15/2015; 195(4): 1364-7. PMID: 26157177, PMCID: PMC4530023, PII: jimmunol.1500904, DOI: 10.4049/jimmunol.1500904, ISSN: 1550-6606.

Diggins KE, Ferrell PB, Irish JM. Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Methods [print-electronic]. 2015 Jul 7/1/2015; 82: 55-63. PMID: 25979346, PMCID: PMC4468028, PII: S1046-2023(15)00199-1, DOI: 10.1016/j.ymeth.2015.05.008, ISSN: 1095-9130.

Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, Alizadeh AA. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2015 Mar 3/10/2015; 112(10): E1116-25. PMID: 25713363, PMCID: PMC4364211, PII: 1501199112, DOI: 10.1073/pnas.1501199112, ISSN: 1091-6490.

Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW. NetworkPainter: dynamic intracellular pathway animation in Cytobank. BMC Bioinformatics. 2015; 16: 172. PMID: 26003204, PMCID: PMC4491883, PII: 10.1186/s12859-015-0602-4, DOI: 10.1186/s12859-015-0602-4, ISSN: 1471-2105.

Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol. Syst. Biol. 2015; 11(10): 835. PMID: 26519361, PMCID: PMC4631206, ISSN: 1744-4292.

Leelatian N, Diggins KE, Irish JM. Characterizing Phenotypes and Signaling Networks of Single Human Cells by Mass Cytometry. Methods Mol. Biol. 2015; 1346: 99-113. PMID: 26542718, PMCID: PMC4656023, DOI: 10.1007/978-1-4939-2987-0_8, ISSN: 1940-6029.

Irish JM. Beyond the age of cellular discovery. Nature immunology. 2014 Dec; 15(12) Sect. 1095,7.

Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS ONE. 2014; 9(7): e100334. PMID: 24983991, PMCID: PMC4077578, PII: PONE-D-13-55136, DOI: 10.1371/journal.pone.0100334, ISSN: 1932-6203.

Irish JM, Doxie DB. High-dimensional single-cell cancer biology. Curr. Top. Microbiol. Immunol. 2014; 377: 1-21. PMID: 24671264, PMCID: PMC4216808, DOI: 10.1007/82_2014_367, ISSN: 0070-217X.

Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA. Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood [print-electronic]. 2013 Feb 2/28/2013; 121(9): 1604-11. PMID: 23297126, PMCID: PMC3587323, PII: blood-2012-09-457283, DOI: 10.1182/blood-2012-09-457283, ISSN: 1528-0020.

Myklebust JH, Irish JM, Brody J, Czerwinski DK, Houot R, Kohrt HE, Timmerman J, Said J, Green MR, Delabie J, Kolstad A, Alizadeh AA, Levy R. High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Blood [print-electronic]. 2013 Feb 2/21/2013; 121(8): 1367-76. PMID: 23297127, PMCID: PMC3578953, PII: blood-2012-04-421826, DOI: 10.1182/blood-2012-04-421826, ISSN: 1528-0020.

Blix ES, Irish JM, Husebekk A, Delabie J, Tierens AM, Myklebust JH, Kolstad A. Altered BCR and CD40 signalling are associated with clinical outcome in small lymphocytic lymphoma/chronic lymphocytic leukaemia and marginal zone lymphoma patients [letter]. Br. J. Haematol [print-electronic]. 2012 Dec; 159(5): 604-8. PMID: 23043253, PMCID: PMC3767388, DOI: 10.1111/bjh.12073, ISSN: 1365-2141.

Blix ES, Irish JM, Husebekk A, Delabie J, Forfang L, Tierens AM, Myklebust JH, Kolstad A. Phospho-specific flow cytometry identifies aberrant signaling in indolent B-cell lymphoma. BMC Cancer. 2012; 12: 478. PMID: 23072591, PMCID: PMC3519597, PII: 1471-2407-12-478, DOI: 10.1186/1471-2407-12-478, ISSN: 1471-2407.

Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R. B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2010 Jul 7/20/2010; 107(29): 12747-54. PMID: 20543139, PMCID: PMC2919949, PII: 1002057107, DOI: 10.1073/pnas.1002057107, ISSN: 1091-6490.

Kotecha N, Krutzik PO, Irish JM. Web-based analysis and publication of flow cytometry experiments. Curr Protoc Cytom. 2010 Jul; Chapter 10: Unit10.17. PMID: 20578106, PMCID: PMC4208272, DOI: 10.1002/0471142956.cy1017s53, ISSN: 1934-9300.

Houot R, Goldstein MJ, Kohrt HE, Myklebust JH, Alizadeh AA, Lin JT, Irish JM, Torchia JA, Kolstad A, Chen L, Levy R. Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. Blood [print-electronic]. 2009 Oct 10/15/2009; 114(16): 3431-8. PMID: 19641184, PMCID: PMC2765679, PII: blood-2009-05-223958, DOI: 10.1182/blood-2009-05-223958, ISSN: 1528-0020.

Hammer MM, Kotecha N, Irish JM, Nolan GP, Krutzik PO. WebFlow: a software package for high-throughput analysis of flow cytometry data. Assay Drug Dev Technol. 2009 Feb; 7(1): 44-55. PMID: 19187010, PMCID: PMC2956679, PII: 10.1089/adt.2008.174, DOI: 10.1089/adt.2008.174, ISSN: 1540-658X.

Kotecha N, Flores NJ, Irish JM, Simonds EF, Sakai DS, Archambeault S, Diaz-Flores E, Coram M, Shannon KM, Nolan GP, Loh ML. Single-cell profiling identifies aberrant STAT5 activation in myeloid malignancies with specific clinical and biologic correlates. Cancer Cell. 2008 Oct 10/7/2008; 14(4): 335-43. PMID: 18835035, PMCID: PMC2647559, PII: S1535-6108(08)00293-6, DOI: 10.1016/j.ccr.2008.08.014, ISSN: 1878-3686.

Van Meter ME, Díaz-Flores E, Archard JA, Passegué E, Irish JM, Kotecha N, Nolan GP, Shannon K, Braun BS. K-RasG12D expression induces hyperproliferation and aberrant signaling in primary hematopoietic stem/progenitor cells. Blood [print-electronic]. 2007 May 5/1/2007; 109(9): 3945-52. PMID: 17192389, PMCID: PMC1874575, PII: blood-2006-09-047530, DOI: 10.1182/blood-2006-09-047530, ISSN: 0006-4971.

Irish JM, Anensen N, Hovland R, Skavland J, Børresen-Dale AL, Bruserud O, Nolan GP, Gjertsen BT. Flt3 Y591 duplication and Bcl-2 overexpression are detected in acute myeloid leukemia cells with high levels of phosphorylated wild-type p53. Blood [print-electronic]. 2007 Mar 3/15/2007; 109(6): 2589-96. PMID: 17105820, PII: blood-2006-02-004234, DOI: 10.1182/blood-2006-02-004234, ISSN: 0006-4971.

Irish JM, Czerwinski DK, Nolan GP, Levy R. Altered B-cell receptor signaling kinetics distinguish human follicular lymphoma B cells from tumor-infiltrating nonmalignant B cells. Blood [print-electronic]. 2006 Nov 11/1/2006; 108(9): 3135-42. PMID: 16835385, PMCID: PMC1895530, PII: blood-2006-02-003921, DOI: 10.1182/blood-2006-02-003921, ISSN: 0006-4971.

Irish JM, Czerwinski DK, Nolan GP, Levy R. Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry. J. Immunol. 2006 Aug 8/1/2006; 177(3): 1581-9. PMID: 16849466, PII: 177/3/1581, ISSN: 0022-1767.

Irish JM, Kotecha N, Nolan GP. Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat. Rev. Cancer. 2006 Feb; 6(2): 146-55. PMID: 16491074, PII: nrc1804, DOI: 10.1038/nrc1804, ISSN: 1474-175X.

Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud Ø, Gjertsen BT, Nolan GP. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell. 2004 Jul 7/23/2004; 118(2): 217-28. PMID: 15260991, PII: S0092867404006282, DOI: 10.1016/j.cell.2004.06.028, ISSN: 0092-8674.

Krutzik PO, Irish JM, Nolan GP, Perez OD. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin. Immunol. 2004 Mar; 110(3): 206-21. PMID: 15047199, PII: S1521661603003097, DOI: 10.1016/j.clim.2003.11.009, ISSN: 1521-6616.

Armstrong JS, Steinauer KK, Hornung B, Irish JM, Lecane P, Birrell GW, Peehl DM, Knox SJ. Role of glutathione depletion and reactive oxygen species generation in apoptotic signaling in a human B lymphoma cell line. Cell Death Differ. 2002 Mar; 9(3): 252-63. PMID: 11859408, DOI: 10.1038/sj.cdd.4400959, ISSN: 1350-9047.